ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGTTTGAAATGTTTGCTGAGGGTGGTGAGTCAGGTTCTGCTGCTGCTGCTGGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCCgtaagtcccaaccgtaccttatgttgtctgctcaactgttgtagatgttgtcccaagtcccaacccttctgtttgtctgacatttggacaatccag

Basic information

species	Zea mays
transcript	AC148152.3_FGT008
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC148152.3_FGT008 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g45710.5 (Oryza sativa), 5'ss of exon 2

------------GGTTTGAAATGTTTGCTGAGGGTGGTGAGTCAGGTTCTGCTGCTGCTGCTGGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCCgtaagt-cccaaccgtaccttatgttgtctgctcaactgttgtaga--tgttgtcccaagtcccaacccttctgtttgtct-gacatttgga--caatccag
            ||||||||||  |||||||| |||| || ||            |||||  || || |  ||||||||||| ||||| |||||||| ||||| || ||||||||||| |   |   ||   | | |  |  ||| |  | |   ||   |||  ||| |||  | || |    ||  |||   | ||  | ||  || | |  
CTATGCTCAGGGGGTTTGAAATTCTTGCTGAGAGTGGAGAATC------------TGCTGGCGGCGATAACTGCAGCCACAATGTTGCTGCTTGGCATAATGTTCCATGCCCgtaagtacatgagtatagaatctctaatgagctaatttatctcagttctgtactccaaagaacaaatctccttgcctgtaaagtcacctagagtcacttc--

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|148971884|gb|EE022650.2|EE022650

EST:     GGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCC                         GCAAGAAAGGCTTAAGTTTTGGTCTGATCCTGATACTGAGTTGAAACTTGC
genomic: GGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCCgtaagtccca ... gacaatccagGCAAGAAAGGCTTAAGTTTTGGTCTGATCCTGATACTGAGTTGAAACTTGC

EST: gi|211331627|gb|FL134113.1|FL134113

EST:     GGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCC                         GCAAGAAAGGCTTAAAGTTT-GGTCTGATCCTGATACTGAGTTGAAACTTG
genomic: GGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCCgtaagtccca ... gacaatccagGCAAGAAAGGCTTAA-GTTTTGGTCTGATCCTGATACTGAGTTGAAACTTG

EST: gi|148945507|gb|EC890751.2|EC890751

EST:     GGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCC                         GCAAGAAAGGCTTAAGTTTTTGGTCTGATCCTGGATACTGAGTTGAAACTT
genomic: GGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCCgtaagtccca ... gacaatccagGCAAGAAAGGCTTAAGTTTT-GGTCTGATCCTG-ATACTGAGTTGAAACTT

EST: gi|148959131|gb|EE010603.2|EE010603

EST:     GGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCC                         GCAAGAAAGGCTTAAGTTTTGGTCTGATCCTGATACTGAGTTGAAACTTGC
genomic: GGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCCgtaagtccca ... gacaatccagGCAAGAAAGGCTTAAGTTTTGGTCTGATCCTGATACTGAGTTGAAACTTGC

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 3 RNA-Seq libraries.

Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 21

GGTTTGAAATGTTTGCTGAGGGTGGTGAGTCAGGTTCTGCTGCTGCTGCTGGTGACAGTTGCAGCCACAACGTTGCGGCTTGGCACAATGTCCCTTGCCCgtaagtccca ... gacaatccagGCAAGAAAGGCTTAAGTTTTGGTCTGATCCTGATACTGAGTTGAAACTTGCTAAGGAAACTGGGATCAGTGTTTTCCGCATGGGGATTGATTGGACGAGG

Block sizes: 29 (upstream exon), 21 (downstream exon)
Score: 1